4C interaction analysis

Question

[Bogdan]

Dear all,

please would you let me know, would you have a recommendation regarding the algorithm to use for 4C data analysis (we do not have replicates).

A few analysis algorithms are listed here on omictools.com : https://omictools.com/4c-analysis-category

thank you !

-- bogdan

[IP]

4Cker gave me some good results a year ago

Answer 1

[IP]

4Cker gave me some good results a year ago. And you can still get some contact maps when you do not have replicates. What I remember is that if your data quality standards are not good (See section 5.2), 4Cker will produce really wrong results. So I suggest:

1- Make sure that your data is good enough (my feeling after analyzing 4C-seq data is that it is really noisy)

2- Go for 4Cker

[Bogdan]

Thank you very much for your suggestions !